BME 210 Lecture 18 Genomics

BME 210 Lecture 18 Genomics - 18. Genomics • Genomics -...

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18. Genomics
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Genomics - analysis of organisms’ entire genomes; identification of all or many genes Functional genomics - global analysis of gene expression; identification of all/many mRNAs Proteomics – global analysis of cell protein content; identification of all/many expressed proteins and their interactions Metabolomics - analysis of all small-molecule metabolites Bioinformatics - computer-aided processing of biological data, data interpretation, structuring, storage, search, detection of interactions
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Genomics tools DNA microarrays • DNA microarrays allow simultaneous detection of thousands of genes (genomics) or mRNAs (functional genomics) • This method is related to FISH and Southern/Northern blotting methods - it is based on hybridization between sampled DNAs or RNAs with complementary DNA probes • A microarray – a 2D array of microscopic spots on a slide with multiple immobilized DNA hybridization probes • Other names – “gene chip”, “DNA chip”, or “gene array”
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DNA Microarray • Each spot has a defined location; it contains immobilized DNA hybridization probes with a known nucleotide sequence • Number of spots: 10 to ≈ 40,000; typical – several thousands • Spot size: down to ≈ 100 m; each spot contains millions of probes • Spot separation ≈ 100 m • Substrate – glass, silicon or plastic slide • Sampled DNAs or RNAs are fluorescently labeled and applied to the slide; they hybridize with the probes and are detected by fluorescence microscopy
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Microarray types 1. “Spotted” microarrays Probes: cDNAs or oligonucleotides cDNAs are obtained from mRNAs by reverse transcription Oligonucleotides are obtained by chemical synthesis Probes are printed and immobilized on a chip surface 2. “Oligonucleotide” microarrays : Probes: only oligonucleotides which are synthesized directly on a chip
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Spotted Microarrays • The DNA probes are placed on a glass by contact printing using an array of fine pins (the most common) or inkjet printing (less common – it is harder to handle a large number of probes) • After printing, probes are linked to the slide by UV irradiation • Contact printing technique can be used to produce "in-house" microarrays customized for each experiment
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BME 210 Lecture 18 Genomics - 18. Genomics • Genomics -...

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